v0.12.6

What's Changed

• Change default appraise by @AroneyS in #142
• Allow normal regex for taxa-of-interest argument by @AroneyS in #143
• Update README.md by @wwood in #144
• Fix enumeration of all combinations before filtering to top 100 by @AroneyS in #145
• Fix suffixes not being removed in preclusters by @AroneyS in #146
• Allow provided assemblies by @AroneyS in #147
• Change prior header to be consistent for single and update by @AroneyS in #148
• Add precluster distances argument by @AroneyS in #150
• Run no genomes in lazy mode by @AroneyS in #151
• Update docs by @AroneyS in #152
• Bump aviary to v0.10.0 by @AroneyS in #153

Full Changelog: v0.12.5...v0.12.6

v0.12.5

What's Changed

• Add separate subcommand for single-assembly by @AroneyS in #140

Full Changelog: v0.12.4...v0.12.5

v0.12.4

New release to match docker release

Full Changelog: v0.12.3...v0.12.4

v0.12.2

What's Changed

• Fix abundance weighting by @AroneyS in #132
• Add coassemblies list arg to update by @AroneyS in #134
• Update polars to v1.x by @AroneyS in #133
• Fix update on output without genomes by @AroneyS in #138
• Download databases by @AroneyS in #121

Full Changelog: v0.12.1...v0.12.2

v0.12.1

Fix pip packaging

Full Changelog: v0.12.0...v0.12.1

v0.12.0

Major changes

• Kmer preclustering allows Bin Chicken to scale beyond 250k samples
• Abundance weighting biases coassembly selection to those estimated to recover highly abundant but unrecovered lineages

What's Changed

• Kmer preselection by @AroneyS in #113
• Restrict sra downloading by @AroneyS in #124
• Add download-limit arg by @AroneyS in #125
• Remove filtering from query processing by @AroneyS in #127
• Switch to sourmash concatenate by @AroneyS in #128
• Abundance weighting by @AroneyS in #129
• Add abundance weighting samples arg by @AroneyS in #130
• Update aviary_commands to match smk rule by @AroneyS in #131

Full Changelog: v0.11.0...v0.12.0

v0.11.0

What's Changed

• fix binchicken suffix trimming by @AroneyS in #118
• Fix nontargets evaluation by @AroneyS in #119
• Error updates by @AroneyS in #120
• Update SingleM to v0.18 by @AroneyS in #123
• Remove GTDBtk from Aviary fast by @AroneyS in #122

Full Changelog: v0.10.5...v0.11.0

v0.10.5

What's Changed

• Update dependencies by @AroneyS in #111
• Fix filter bam naming bug by @AroneyS in #112 (Thanks Andy Leu)
• Fix tmpdir by @AroneyS in #114
• Harden evaluate by @AroneyS in #116
• Add coverage to evaluate by @AroneyS in #117
• Update Aviary by @AroneyS in #115

Full Changelog: v0.10.4...v0.10.5

v0.10.4

What's Changed

• Add doctave-based docs by @AroneyS in #101
• bin: Improve help msgs. by @wwood in #102
• Improve snakemake retry behaviour by @AroneyS in #105
• Reduce update required inputs by @AroneyS in #106
• fix COASSEMBLY_SAMPLES causing lengths to get out of sync by @AroneyS in #107
• Improve Aviary running by @AroneyS in #108
• Notify if any sample skipped by @AroneyS in #109
• Update improvements by @AroneyS in #110

New Contributors

• @wwood made their first contribution in #102

Full Changelog: v0.10.3...v0.10.4

v0.10.3

What's Changed

• Add links and citation by @AroneyS in #100

Full Changelog: v0.10.2...v0.10.3